Seriola species, collectively known as amberjacks, are fish of particular interest to the growing aquaculture industry due to their high value, forming a billion dollar plus component of the sashimi industry. Of these species, the native California Seriola dorsalis is considered a prime candidate for aquaculture development in southern California. Although production from broodstock populations has been successful, it has not yet reached a sustainable level where it can satisfy the aquaculture demand, largely due to difficulties from highly variable survival and growth rates through the larval stages. Given the major physical changes that occur during the earliest life stages, one way to examine variability in survival and growth is at the gene and molecular levels across those early-developmental periods. Transcriptome analyses, using RNA-Seq, were conducted to characterize physiological system development and examine growth heterogeneity in larval yellowtail. Gene expression was measured in three replicates of pooled larval samples at 2, 7, and 17 days post hatch (dph) for larvae categorized as fast- or slow-growing. An average of sixty million reads was obtained per replicate; genes of related function were then sorted into clusters and those found at high frequency in the differential gene expression set were identified. Differences in molecular pathways, biological processes, and gene regulating patterns between the two fitness groups were examined. There were many differentially expressed genes across developmental stages and between the fitness groups, for example, genes involved in oxidative phosphorylation pathways revealed interesting patterns both across developmental stages and between slow- and fast-growing larvae. Results of these analyses will be presented.